SMED30022585

Overview
NameSMED30022585
Smed IDSMED30022585
Length (bp)862
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 



 

Overview

 

Single cell RNA-seq of pluripotent neoblasts and its early progenies


We isolated X1 neoblasts cells enriched in high piwi-1 expression (Neoblast Population), and profiled ∼7,614 individual cells via scRNA-seq. Unsupervised analyses uncovered 12 distinct classes from 7,088 high-quality cells. We designated these classes Nb1 to Nb12 and ordered them based on high (Nb1) to low (Nb12) piwi-1 expression levels. We further defined groups of genes that best classified the cells parsed into 12 distinct cell clusters to generate a scaled expression heat map of discriminative gene sets for each cluster. Expression of each cluster’s gene signatures was validated using multiplex fluorescence in situ hybridization (FISH) co-stained with piwi-1 and largely confirmed the cell clusters revealed by scRNA-seq.

We also tested sub-lethal irradiation exposure. To profile rare pluripotent stem cells (PSCs) and avoid interference from immediate progenitor cells, we determined a time point after sub-lethal irradiation (7 DPI) with minimal piwi-1+ cells, followed by isolation and single-cell RNA-seq of 1,200 individual cells derived from X1 (Piwi-1 high) and X2 (Piwi-1 low) cell populations (Sub-lethal Irradiated Surviving X1 and X2 Cell Population)




Explore this single cell expression dataset with our NB Cluster Shiny App




Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

t-SNE plot of surviving X1 and X2 cells (n = 1,039 after QC filter) after sub-lethal irradiation. Colors indicate unbiased cell classification via graph-based clustering. SL, sub-lethal irradiated cell groups.

Expression of SMED30022585 (SMED30022585) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30022585 (SMED30022585) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

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Embryonic Expression

Davies et. al., 2017




Hover the mouse over a column in the graph to view average RPKM values per sample.
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Embryonic Stages: Y: yolk. S2-S8: Stages 2-8. C4: asexual adult. SX: virgin, sexually mature adult.
For further information about sample preparation and analysis for the single animal RNA-Seq experiment, please refer to the Materials and Methods

 

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Anatomical Expression

PAGE et. al., 2020




SMED30022585

has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGE



PAGE Curations: 7

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
headSMED30022585SMESG000021277.1 SmedASXL_000724SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
headSMED30022585SMESG000021277.1 SmedASXL_000300SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
neuronSMED30022585SMESG000021277.1 dd_Smed_v4_16056_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30022585SMESG000021277.1 dd_Smed_v4_16056_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
anterior region of the whole animalSMED30022585SMESG000021277.1 dd_Smed_v4_16056_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
medial muscle cellSMED30022585SMESG000021277.1 dd_Smed_v4_16056_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
headSMED30022585SMESG000021277.1 dd_Smed_v6_16056_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of SMED30022585 vs. Planmine SMEST
Match: SMESG000021277.1 (SMESG000021277.1)

HSP 1 Score: 404.445 bits (1038), Expect = 1.051e-150
Identity = 195/198 (98.48%), Postives = 197/198 (99.49%), Query Frame = -2
Query:    1 HGSMVVTSPNHRTQAPMINYTPNHSTSICYQTNTLQKDKVLMYPSSIDGNHLNQTLPSHTQQNISPNQSIHNNSSQIPYSSLLNRSNIVNSQVPPEIPISSTGIQLQLSPIQLPHESDLTYAAGGLLIPVNHLTDHINYSSSKSGPEYYQPNHQTYPKFLDDRYLSSEKEKYPNTLAYSISYSGTIPHYRQALYTRND 594
            HGSMVVTSPNHRTQAPMINYTPNHSTSICYQTNTLQ+DKVLMYPSSIDGNHLNQTLPSHTQQNIS NQSIHNNSSQIPY+SLLNRSNIVNSQVPPEIPISSTGIQLQLSPIQLPHESDLTYAAGGLLIPVNHLTDHINYSSSKSGPEYYQPNHQTYPKFLDDRYLSSEKEKYPNTLAYSISYSGTIPHYRQALYTRND
Sbjct: 1302 HGSMVVTSPNHRTQAPMINYTPNHSTSICYQTNTLQRDKVLMYPSSIDGNHLNQTLPSHTQQNISLNQSIHNNSSQIPYTSLLNRSNIVNSQVPPEIPISSTGIQLQLSPIQLPHESDLTYAAGGLLIPVNHLTDHINYSSSKSGPEYYQPNHQTYPKFLDDRYLSSEKEKYPNTLAYSISYSGTIPHYRQALYTRND 1499          

HSP 2 Score: 148.288 bits (373), Expect = 1.051e-150
Identity = 72/72 (100.00%), Postives = 72/72 (100.00%), Query Frame = -1
Query:  602 AFYLRKRRNKSHQNSNQNKIENSLGYMQCSNMEMYPTLNPNTRGSSINEISTNNSQRSLDSIKNNFKNNIDQ 817
            AFYLRKRRNKSHQNSNQNKIENSLGYMQCSNMEMYPTLNPNTRGSSINEISTNNSQRSLDSIKNNFKNNIDQ
Sbjct: 1229 AFYLRKRRNKSHQNSNQNKIENSLGYMQCSNMEMYPTLNPNTRGSSINEISTNNSQRSLDSIKNNFKNNIDQ 1300          
BLAST of SMED30022585 vs. Planmine SMEST
Match: SMESG000021277.1 (SMESG000021277.1)

HSP 1 Score: 404.445 bits (1038), Expect = 1.275e-150
Identity = 195/198 (98.48%), Postives = 197/198 (99.49%), Query Frame = -2
Query:    1 HGSMVVTSPNHRTQAPMINYTPNHSTSICYQTNTLQKDKVLMYPSSIDGNHLNQTLPSHTQQNISPNQSIHNNSSQIPYSSLLNRSNIVNSQVPPEIPISSTGIQLQLSPIQLPHESDLTYAAGGLLIPVNHLTDHINYSSSKSGPEYYQPNHQTYPKFLDDRYLSSEKEKYPNTLAYSISYSGTIPHYRQALYTRND 594
            HGSMVVTSPNHRTQAPMINYTPNHSTSICYQTNTLQ+DKVLMYPSSIDGNHLNQTLPSHTQQNIS NQSIHNNSSQIPY+SLLNRSNIVNSQVPPEIPISSTGIQLQLSPIQLPHESDLTYAAGGLLIPVNHLTDHINYSSSKSGPEYYQPNHQTYPKFLDDRYLSSEKEKYPNTLAYSISYSGTIPHYRQALYTRND
Sbjct:  656 HGSMVVTSPNHRTQAPMINYTPNHSTSICYQTNTLQRDKVLMYPSSIDGNHLNQTLPSHTQQNISLNQSIHNNSSQIPYTSLLNRSNIVNSQVPPEIPISSTGIQLQLSPIQLPHESDLTYAAGGLLIPVNHLTDHINYSSSKSGPEYYQPNHQTYPKFLDDRYLSSEKEKYPNTLAYSISYSGTIPHYRQALYTRND 853          

HSP 2 Score: 147.902 bits (372), Expect = 1.275e-150
Identity = 72/72 (100.00%), Postives = 72/72 (100.00%), Query Frame = -1
Query:  602 AFYLRKRRNKSHQNSNQNKIENSLGYMQCSNMEMYPTLNPNTRGSSINEISTNNSQRSLDSIKNNFKNNIDQ 817
            AFYLRKRRNKSHQNSNQNKIENSLGYMQCSNMEMYPTLNPNTRGSSINEISTNNSQRSLDSIKNNFKNNIDQ
Sbjct:  583 AFYLRKRRNKSHQNSNQNKIENSLGYMQCSNMEMYPTLNPNTRGSSINEISTNNSQRSLDSIKNNFKNNIDQ 654          
The following BLAST results are available for this feature:
BLAST of SMED30022585 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30022585 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30022585 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30022585 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30022585 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30022585 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30022585 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30022585 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30022585 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30022585 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30022585 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30022585 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30022585 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30022585 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000021277.11.051e-15098.48SMESG000021277.1[more]
SMESG000021277.11.275e-15098.48SMESG000021277.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30022585 ID=SMED30022585|Name=SMED30022585|organism=Schmidtea mediterranea sexual|type=transcript|length=862bp
ATCGTTTCTAGTATACAAAGCTTGGCGGTAATGCGGTATGGTACCAGAAT
AGGAAATTGAATACGCAAGAGTGTTTGGATATTTTTCTTTTTCACTTGAT
AAATATCTGTCATCAAGAAACTTTGGATAAGTTTGATGATTAGGTTGATA
ATATTCTGGACCAGATTTAGAAGAAGAGTAGTTGATGTGGTCAGTTAGGT
GGTTGACTGGAATGAGCAATCCACCTGCTGCATAAGTTAGATCTGACTCG
TGAGGTAATTGGATTGGAGATAATTGCAGTTGAATTCCAGTTGAGCTGAT
CGGAATCTCTGGTGGGACCTGTGAATTTACTATATTCGATCTGTTTAGAA
GAGAGGAGTAAGGGATCTGAGAAGAATTGTTGTGGATGGATTGGTTCGGT
GAAATATTCTGTTGAGTATGGGAGGGTAAGGTCTGGTTTAGGTGATTGCC
ATCGATTGATGAAGGGTACATAAGAACTTTGTCTTTCTGCAGCGTATTGG
TCTGATAACAAATCGAGGTTGAGTGGTTGGGGGTATAGTTTATCATTGGT
GCCTGAGTGCGATGATTTGGACTTGTCACTACCATAGATCCATGAAGCTT
CTTGATCAATATTGTTTTTAAAATTATTTTTAATACTATCTAAACTTCTC
TGAGAATTGTTTGTCGAGATTTCGTTGATTGAGGAACCTCGCGTGTTTGG
GTTGAGGGTTGGGTACATTTCCATGTTTGAGCACTGCATGTAACCTAAAG
AATTTTCAATTTTGTTTTGATTTGAATTTTGATGTGATTTGTTTCTTCTT
TTTCGTAAATAAAAAGCAACAAACAAAATATTGATCACAAGAATGACAAA
AACAAAAACTCA
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protein sequence of SMED30022585-orf-1

>SMED30022585-orf-1 ID=SMED30022585-orf-1|Name=SMED30022585-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=195bp
MVVTSPNHRTQAPMINYTPNHSTSICYQTNTLQKDKVLMYPSSIDGNHLN
QTLPSHTQQNISPNQSIHNNSSQIPYSSLLNRSNIVNSQVPPEIPISSTG
IQLQLSPIQLPHESDLTYAAGGLLIPVNHLTDHINYSSSKSGPEYYQPNH
QTYPKFLDDRYLSSEKEKYPNTLAYSISYSGTIPHYRQALYTRND
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000101muscle cell
PLANA:0000140anterior region of the whole animal
PLANA:0000418head
PLANA:0002056medial muscle cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 4..18